Implemented CIGAR representation of an Alignment view for passing to

[jalview.git] / src / jalview / gui / AlignViewport.java

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 3ae0a52..af59388 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1204,6 +1204,87 @@ public class AlignViewport
       return sequences;\r
     }\r
 \r
+    /**\r
+     * This method returns the visible alignment as text, as\r
+     * seen on the GUI, ie if columns are hidden they will not\r
+     * be returned in the result.\r
+     * Use this for calculating trees, PCA, redundancy etc on views\r
+     * which contain hidden columns.\r
+     * @return String[]\r
+     */\r
+    public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)\r
+    {\r
+      CigarArray selection=null;\r
+      SequenceI [] seqs= null;\r
+      int i, iSize;\r
+      int start = 0, end = 0;\r
+      if(selectedRegionOnly && selectionGroup!=null)\r
+      {\r
+        iSize = selectionGroup.getSize(false);\r
+        seqs = selectionGroup.getSequencesInOrder(alignment);\r
+        start = selectionGroup.getStartRes();\r
+        end = selectionGroup.getEndRes()+1;\r
+      }\r
+      else\r
+      {\r
+        iSize = alignment.getHeight();\r
+        seqs = alignment.getSequencesArray();\r
+        end = alignment.getWidth();\r
+      }\r
+      SeqCigar[] selseqs = new SeqCigar[iSize];\r
+      for(i=0; i<iSize; i++)\r
+      {\r
+        selseqs[i] = new SeqCigar(seqs[i], start, end);\r
+      }\r
+      selection=new CigarArray(selseqs);\r
+\r
+      int[] hiddenregions = null;\r
+      char[] hr_ops = null;\r
+      if (hasHiddenColumns) {\r
+        Vector _hiddenregions = new Vector();\r
+        Vector regions = colSel.getHiddenColumns();\r
+        int blockStart = start, blockEnd=end;\r
+        int [] region;\r
+        int hideStart, hideEnd;\r
+        int last=start;\r
+        for (int j = 0; last<end & j < regions.size(); j++)\r
+        {\r
+          region = (int[]) regions.elementAt(j);\r
+          hideStart = region[0];\r
+          hideEnd = region[1];\r
+          // edit hidden regions to selection range\r
+          if(hideStart<last) {\r
+            if (hideEnd > last)\r
+            {\r
+              hideStart = last;\r
+            } else\r
+              continue;\r
+          }\r
+\r
+          if (hideStart>end)\r
+            break;\r
+\r
+          if (hideEnd>end)\r
+            hideEnd=end;\r
+\r
+          if (hideStart>hideEnd)\r
+            break;\r
+          /**\r
+           * form operations...\r
+           */\r
+          if (last<hideStart)\r
+            selection.addOperation(CigarArray.M, hideStart-last);\r
+          selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);\r
+          last = hideEnd+1;\r
+        }\r
+        // Final match if necessary.\r
+        if (last<end)\r
+          selection.addOperation(CigarArray.M, end-last);\r
+      } else {\r
+        selection.addOperation(CigarArray.M, end-start);\r
+      }\r
+      return selection;\r
+    }\r
 \r
     /**\r
      * This method returns the visible alignment as text, as\r